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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tacagccactagttttctctatcaagtatacttatattatgtattaaggtcacagcagcttcgcttatattatgaactcacattcacctttgccttccagCTAAGATGGCGAAACTGAAGGAGTTGTTGCAAAAGAGTGAAAACCACATTTGTGCTGACTGTGGTGCATCTGATCCCAAATGGGC

Basic information

species Zea mays
transcript GRMZM2G138349_T03
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G138349_T02 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os02g10480.4 (Oryza sativa), 3'ss of exon 2
----------------------------------------------------------------tacagccactagttttctctatcaagtatacttatattatgtattaaggtcacagcagcttcgcttatattatgaactcacatt-cacctttgccttccagCTAAGATGGCGAAACTGAAGGAGTTGTTGCAAAAGAGTGAAAACCACATTTGTGCTGACTGTGGTGCATCTGATCCCAAATGGGC
                                                                | ||   |||||||| |||| |  |||      | || |  | ||   |    || || |   |||  || ||||| ||| ||| ||  |||  | | ||||||||||||| |||||||||||| | ||||| |  ||||||||||  || |||||||||||  | ||  |||| |||||||||||
gtgaccaaaaacaaaattctgcaacttcttggagtacttcagatttggtcattttcaatgggtgtgcatttactagtttgctcttt--agtgctgacagataagattttgccggtggagaaggt---cttgcatgatgaattcatatttcatttttctcatgcagCTAAGATGGCAAAACTGAAGGAGCTATTGCACAGAAGTGAAAACCGTATCTGTGCTGACTGCAGCGCGCCTGACCCCAAATGGGC

upper sequence: GRMZM2G138349_T02 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os02g10480.3 (Oryza sativa), 3'ss of exon 3
----tacagccactagttttctctatcaagtatacttatattatgtattaaggtcacagcagcttcgcttatattatgaactcacatt-cacctttgccttccagCTAAGATGGCGAAACTGAAGGAGTTGTTGCAAAAGAGTGAAAACCACATTTGTGCTGACTGTGGTGCATCTGATCCCAAATGGGC
    | ||   |||||||| |||| |  |||      | || |  | ||   |    || || |   |||  || ||||| ||| ||| ||  |||  | | ||||||||||||| |||||||||||| | ||||| |  ||||||||||  || |||||||||||  | ||  |||| |||||||||||
ggtgtgcatttactagtttgctcttt--agtgctgacagataagattttgccggtggagaaggt---cttgcatgatgaattcatatttcatttttctcatgcagCTAAGATGGCAAAACTGAAGGAGCTATTGCACAGAAGTGAAAACCGTATCTGTGCTGACTGCAGCGCGCCTGACCCCAAATGGGC
















Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|60672574|gb|DN475276.1|DN475276
EST:     GAGCTTTCTTGCACCCAAGATGAGTGGGCATGGTGACACTGCGACCTCAG                         CTAAGATGGCGAAACTGAAGGAGTTGTTGCAAAAGAGTGAAAACCACATTT
genomic: GAGCTTTCTTGCACCCAAGATGAGTGGGCATGGTGACACTGCGACCTCAGgtatgcgtaa ... tgccttccagCTAAGATGGCGAAACTGAAGGAGTTGTTGCAAAAGAGTGAAAACCACATTT
EST: gi|211169837|gb|FK962697.1|FK962697
EST:     GAGCTTTCTTGCACCCAAGATGAGTGGGCATGGTGACACTGCGACCTCAG                         CTAAGATGGCGAAACTGAAGGAGTTGTTGCAAAAGANTGAAAACCACATTT
genomic: GAGCTTTCTTGCACCCAAGATGAGTGGGCATGGTGACACTGCGACCTCAGgtatgcgtaa ... tgccttccagCTAAGATGGCGAAACTGAAGGAGTTGTTGCAAAAGAGTGAAAACCACATTT
EST: gi|211166491|gb|FK962680.1|FK962680
EST:     GAGCTTTCTTGCACCCAAGATGAGTGGGCATGGTGACACTGCGACCTCAG                         CTAAGATGGCGAAACTGAAGGAGTTGTTGCAAAAGAGTGAAAACCACATTT
genomic: GAGCTTTCTTGCACCCAAGATGAGTGGGCATGGTGACACTGCGACCTCAGgtatgcgtaa ... tgccttccagCTAAGATGGCGAAACTGAAGGAGTTGTTGCAAAAGAGTGAAAACCACATTT
EST: gi|211169840|gb|FK962700.1|FK962700
EST:     GAGCTTTCTTGCACCCAAGATGAGTGGGCATGGTGACACTGCGACCTCAG                         CTAAGATGGCGATACTGAAGGAGTTGTTGCAAAAGAGTGAAAACCACATTT
genomic: GAGCTTTCTTGCACCCAAGATGAGTGGGCATGGTGACACTGCGACCTCAGgtatgcgtaa ... tgccttccagCTAAGATGGCGAAACTGAAGGAGTTGTTGCAAAAGAGTGAAAACCACATTT
EST: gi|211168166|gb|FK962693.1|FK962693
EST:     GAGCTTTCTTGCACCCAAGATGAGTGGGCATGGTGACACTGCGACCTCAG                         CTAAGATGGCGAAACTGAAGGAGTTGTTGCAAAAGAGTGAAAACCACATTT
genomic: GAGCTTTCTTGCACCCAAGATGAGTGGGCATGGTGACACTGCGACCTCAGgtatgcgtaa ... tgccttccagCTAAGATGGCGAAACTGAAGGAGTTGTTGCAAAAGAGTGAAAACCACATTT
EST: gi|211168168|gb|FK962695.1|FK962695
EST:     GAGCTTTCTTGCACCCAAGATGAGTGGGCATGGTGACACTGCGACCTCAG                         CTAAGATGGCGAAACTGAAGGAGTTGTTGCAAAAGAGTGAAAACCACATTT
genomic: GAGCTTTCTTGCACCCAAGATGAGTGGGCATGGTGACACTGCGACCTCAGgtatgcgtaa ... tgccttccagCTAAGATGGCGAAACTGAAGGAGTTGTTGCAAAAGAGTGAAAACCACATTT
EST: gi|211168157|gb|FK962684.1|FK962684
EST:     GAGCTTTCTTGCACCCAAGATGAGTGGGCATGGTGACACTGCGACCTCAG                         CTAAGATGGCGAAACTGAAGGAGTTGTTGCAAAAGAGTGAAAACCACATTT
genomic: GAGCTTTCTTGCACCCAAGATGAGTGGGCATGGTGACACTGCGACCTCAGgtatgcgtaa ... tgccttccagCTAAGATGGCGAAACTGAAGGAGTTGTTGCAAAAGAGTGAAAACCACATTT
EST: gi|211168159|gb|FK962686.1|FK962686
EST:     GAGCTTTCTTGCACCCAAGATGAGTGGGCATGGTGACACTGCGACCTCAG                         CTAAGATGGCGAAACTGAAGGAGTTGTTGCAAAAGAGTGAAAACCACATTT
genomic: GAGCTTTCTTGCACCCAAGATGAGTGGGCATGGTGACACTGCGACCTCAGgtatgcgtaa ... tgccttccagCTAAGATGGCGAAACTGAAGGAGTTGTTGCAAAAGAGTGAAAACCACATTT
EST: gi|71768791|gb|DR966728.1|DR966728
EST:     GAGCTTTCTTGCACCCAAGATGAGTGGGCATGGTGACACTGCGACCTCAG                         CTAAGATGGCGAAACTGAAGGAGTTGTTGCAAAAGAGTGAAAACCACATTT
genomic: GAGCTTTCTTGCACCCAAGATGAGTGGGCATGGTGACACTGCGACCTCAGgtatgcgtaa ... tgccttccagCTAAGATGGCGAAACTGAAGGAGTTGTTGCAAAAGAGTGAAAACCACATTT
EST: gi|211169838|gb|FK962698.1|FK962698
EST:     GAGCTTTCTTGCACCCAAGATGAGTGGGCATGGTGACACTGCGACCTCAG                         CTAAGATGGCGAAACTGAAGGAGTTGTTGCAAAAGAGTGAAAACCACATTT
genomic: GAGCTTTCTTGCACCCAAGATGAGTGGGCATGGTGACACTGCGACCTCAGgtatgcgtaa ... tgccttccagCTAAGATGGCGAAACTGAAGGAGTTGTTGCAAAAGAGTGAAAACCACATTT
EST: gi|211168160|gb|FK962687.1|FK962687
EST:     GAGCTTTCTTGCACCCAAGATGAGTGGGCATGGTGACACTGCGACCTCAG                         CTAAGATGGCGAAACTGAAGGAGTTGTTGCAAAAGAGTGAAAACCACATTT
genomic: GAGCTTTCTTGCACCCAAGATGAGTGGGCATGGTGACACTGCGACCTCAGgtatgcgtaa ... tgccttccagCTAAGATGGCGAAACTGAAGGAGTTGTTGCAAAAGAGTGAAAACCACATTT
EST: gi|211168169|gb|FK962696.1|FK962696
EST:     GAGCTTTCTTGCACCCAAGATGAGTGGGCATGGTGACACTGCGACCTCAG                         CTAAGATGGCGAAACTGAAGGAGTTGTTGCAAAAGAGTGAAAACCACATTT
genomic: GAGCTTTCTTGCACCCAAGATGAGTGGGCATGGTGACACTGCGACCTCAGgtatgcgtaa ... tgccttccagCTAAGATGGCGAAACTGAAGGAGTTGTTGCAAAAGAGTGAAAACCACATTT
EST: gi|211168161|gb|FK962688.1|FK962688
EST:     GAGCTTTCTTGCACCCAAGATGAGTGGGCATGGTGACACTGCGACCTCAG                         CTAAGATGGCGAAACTGAAGGAGTTGTTGCAAAAGAGTGAAAACCACATTT
genomic: GAGCTTTCTTGCACCCAAGATGAGTGGGCATGGTGACACTGCGACCTCAGgtatgcgtaa ... tgccttccagCTAAGATGGCGAAACTGAAGGAGTTGTTGCAAAAGAGTGAAAACCACATTT
EST: gi|211168164|gb|FK962691.1|FK962691
EST:     GAGCTTTCTTGCACCCAAGATGAGTGGGCATGGTGACACTGCGACCTCAG                         CTAAGATGGCGAAACTGAAGGAGTTGTTGCAAAAGAGTGAAAACCACATTT
genomic: GAGCTTTCTTGCACCCAAGATGAGTGGGCATGGTGACACTGCGACCTCAGgtatgcgtaa ... tgccttccagCTAAGATGGCGAAACTGAAGGAGTTGTTGCAAAAGAGTGAAAACCACATTT
EST: gi|211166492|gb|FK962681.1|FK962681
EST:     GAGCTTTCTTGCACCCAAGATGAGTGGGCATGGTGACACTGCGACCTCAG                         CTAAGATGGCGAAACTGAAGGAGTTGTTGCAAAAGAGTGAAAACCACATTT
genomic: GAGCTTTCTTGCACCCAAGATGAGTGGGCATGGTGACACTGCGACCTCAGgtatgcgtaa ... tgccttccagCTAAGATGGCGAAACTGAAGGAGTTGTTGCAAAAGAGTGAAAACCACATTT
EST: gi|211168167|gb|FK962694.1|FK962694
EST:     GAGCTTTCTTGCACCCAAGATGAGTGGGCATGGTGACACTGCGACCTCAG                         CTAAGATGGCGAAACTGAAGGAGTTGTTGCAAAAGAGTGAAAACCACATTT
genomic: GAGCTTTCTTGCACCCAAGATGAGTGGGCATGGTGACACTGCGACCTCAGgtatgcgtaa ... tgccttccagCTAAGATGGCGAAACTGAAGGAGTTGTTGCAAAAGAGTGAAAACCACATTT
EST: gi|211168165|gb|FK962692.1|FK962692
EST:     GAGCTTTCTTGCACCCAAGATGAGTGGGCATGGTGACACTGCGACCTCAG                         CTAAGATGGCGAAACTGAAGGAGTTGTTGCAAAAGAGTGAAAACCACATTT
genomic: GAGCTTTCTTGCACCCAAGATGAGTGGGCATGGTGACACTGCGACCTCAGgtatgcgtaa ... tgccttccagCTAAGATGGCGAAACTGAAGGAGTTGTTGCAAAAGAGTGAAAACCACATTT
EST: gi|31250107|gb|CD219131.1|CD219131
EST:     GAGCTTTCTTGCACCCAAGATGAGTGGGCATGGTGACACTGCGACCTCAG                         CTAAGATGGCGAAACTGAAGGAGTTGTTGCAAAAGAGTGAAAACCACATTT
genomic: GAGCTTTCTTGCACCCAAGATGAGTGGGCATGGTGACACTGCGACCTCAGgtatgcgtaa ... tgccttccagCTAAGATGGCGAAACTGAAGGAGTTGTTGCAAAAGAGTGAAAACCACATTT
EST: gi|211168163|gb|FK962690.1|FK962690
EST:     GAGCTTTCTTGCACCCAAGATGAGTGGGCATGGTGACACTGCGACCTCAG                         CTAAGATGGCGAAACTGAAGGAGTTGTTGCAAAAGAGTGAAAACCACATTT
genomic: GAGCTTTCTTGCACCCAAGATGAGTGGGCATGGTGACACTGCGACCTCAGgtatgcgtaa ... tgccttccagCTAAGATGGCGAAACTGAAGGAGTTGTTGCAAAAGAGTGAAAACCACATTT
EST: gi|50334443|gb|CO529569.1|CO529569
EST:     GAGCTTTCTTGCACCCAAGATGAGTGGGCATGGTGACACTGCGACCTCAG                         CTAAGATGGCGAAACTGAAGGAGTTGTTGCAAAAGAGTGAAAACCACATTT
genomic: GAGCTTTCTTGCACCCAAGATGAGTGGGCATGGTGACACTGCGACCTCAGgtatgcgtaa ... tgccttccagCTAAGATGGCGAAACTGAAGGAGTTGTTGCAAAAGAGTGAAAACCACATTT
EST: gi|211168162|gb|FK962689.1|FK962689
EST:     GAGCTTTCTTGCACCCAAGATGAGTGGGCATGGTGACACTGCGACCTCAG                         CTAAGATGGCGAAACTGAAGGAGTTGTTGCAAAAGAGTGAAAACCACATTT
genomic: GAGCTTTCTTGCACCCAAGATGAGTGGGCATGGTGACACTGCGACCTCAGgtatgcgtaa ... tgccttccagCTAAGATGGCGAAACTGAAGGAGTTGTTGCAAAAGAGTGAAAACCACATTT
EST: gi|78087464|gb|DV515857.1|DV515857
EST:     GAGCTTTCTTGCACCCAAGATGAGTGGGCATGGTGACACTGCGACCTCAG                         CTAAGATGGCGAAACTGAAGGAGTTGTTGCAAAAGAGTGAAAACCACATTT
genomic: GAGCTTTCTTGCACCCAAGATGAGTGGGCATGGTGACACTGCGACCTCAGgtatgcgtaa ... tgccttccagCTAAGATGGCGAAACTGAAGGAGTTGTTGCAAAAGAGTGAAAACCACATTT
EST: gi|211168156|gb|FK962683.1|FK962683
EST:     GAGCTTTCTTGCACCCAAGATGAGTGGGCATGGTGACACTGCGACCTCAG                         CTAAGATGGCGAAACTGAAGGAGTTGTTGCAAAAGAGTGAAAACCACATTT
genomic: GAGCTTTCTTGCACCCAAGATGAGTGGGCATGGTGACACTGCGACCTCAGgtatgcgtaa ... tgccttccagCTAAGATGGCGAAACTGAAGGAGTTGTTGCAAAAGAGTGAAAACCACATTT

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 4 RNA-Seq libraries.


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 48

GATTGAGTACGATTTGACGCATTTGCGGCCGAGCTTTCTTGCACCCAAGATGAGTGGGCATGGTGACACTGCGACCTCAGgtatgcgtaa ... tgccttccagCTAAGATGGCGAAACTGAAGGAGTTGTTGCAAAAGAGTGAAAACCACATTTGTGCTGACTGTGGTGCATCTGATCCCAAATGGGC


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 99

GATTGAGTACGATTTGACGCATTTGCGGCCGAGCTTTCTTGCACCCAAGATGAGTGGGCATGGTGACACTGCGACCTCAGgtatgcgtaa ... tgccttccagCTAAGATGGCGAAACTGAAGGAGTTGTTGCAAAAGAGTGAAAACCACATTTGTGCTGACTGTGGTGCATCTGATCCCAAATGGGC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 93

GATTGAGTACGATTTGACGCATTTGCGGCCGAGCTTTCTTGCACCCAAGATGAGTGGGCATGGTGACACTGCGACCTCAGgtatgcgtaa ... tgccttccagCTAAGATGGCGAAACTGAAGGAGTTGTTGCAAAAGAGTGAAAACCACATTTGTGCTGACTGTGGTGCATCTGATCCCAAATGGGC


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 82

GATTGAGTACGATTTGACGCATTTGCGGCCGAGCTTTCTTGCACCCAAGATGAGTGGGCATGGTGACACTGCGACCTCAGgtatgcgtaa ... tgccttccagCTAAGATGGCGAAACTGAAGGAGTTGTTGCAAAAGAGTGAAAACCACATTTGTGCTGACTGTGGTGCATCTGATCCCAAATGGGC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaggtcacagcagcttcgcttatattatgaactcacattcacctttgccttccagCTAAGATGGCGAAACTGAAGGAGTTGTTGCAAAAGAGTGAAAACCACATTTGTGCTGACTGTGGTGCATCTGATCCCAAATGGGC
                             aactcac  putative branch site (score: 82)
                                     ttcacctttgccttcc  CT-rich tract
                   ttatattatgaact  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tacagccactagttttctctatcaagtatacttatattatgtattaaggtcacagcagcttcgcttatattatgaactcacattcacctttgccttccagCTAAGATGGCGAAACTGAAGGAGTTGTTGCAAAAGAGTGAAAACCACATTTGTGCTGACTGTGGTGCATCTGATCCCAAATGGGC

- - gccacta
- - - - - - - - - - - - - - - - - - -tatgtat
- - - - - - - - - - - - - - - - - - - - - - - - - -acagcag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cattcac